I hadn't noticed the ST-10XME camera in your signature but that being the case the workflow should be something along the lines of:
Calibrate all images with master darks and bias frames. (I save after each giving meaningful extensions to indicate their state such as m101-L-001_c, for calibarted, and so on)
Possible Cosmetic Correction if needed
Reject all bad images
Align all like binned images (if they are all 1x1, align all at one time and save again)
Use appropriate Image Integration method to produce master frames, save (m101-L-19, showing master L from 19 frames)
Use Color Combine or LRGB to make master RGB image, save again (ie: m101-rgb-121312, indicates 12 red, 13, green, and 12 blue frames used)
Process such as Dynamic Crop to get rid of the overlapping edges and save
Process the RGB master such as DBE, Masked Stretch or Histogram Stretch, noise and so on, save.
Process the master Lum as well, Dynamic Crop, DBE, stretch, noise, and so on,save
When happy with the 2 master frames, use Dynamic Align to align images. I use stars from all over the image, all corners, middle, and so on, in this case maybe 8-10 stars to align. Save each
Use LRGB combine to make LRGB image. uncheck all image boxes except the L, populate that image in the dialog, and then drag the triangle over the RGB image to combine.
This is all very basic and there are many processes that could be used in between depending on tastes and quality of data. That's where you develop your own style and routines.
HTH,
Steve